Getting back to the question of how the Jaguar failed:
Al's explanation of the desoldered current shunt resistor would make sense, except that the Jaguar says it's outputting 0v.
I re-checked the diagram: the Jaguar measures its supply voltage, but not its output voltage. The output voltage is calculated from duty cycle. (Indeed, in the first revisions of the firmware, the output voltage was only GIVEN in duty cycle, on a range of -1 to 1.)
Apparently nobody has had this exact issue before.
I will check that the resistor is still connected, but I will also try reflashing the Jaguar, in case the firmware got corrupted.
More info on the over-current: the Jaguar goes into over-current fault at 60A after 2 seconds. I was running an
RS-775. (There were some binding issues with the jack screw on our arm)